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- PDB-7lk8: Crystal structure of KPC-2 T215P mutant -

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Basic information

Entry
Database: PDB / ID: 7lk8
TitleCrystal structure of KPC-2 T215P mutant
ComponentsBeta-lactamase
KeywordsHYDROLASE / KPC / Carbapenemase / Beta-lactamase / Antibiotic Resistance / Enzyme / Beta-lactam / antibiotics
Function / homology
Function and homology information


beta-lactam antibiotic catabolic process / beta-lactamase / beta-lactamase activity / response to antibiotic
Similarity search - Function
Beta-lactamase class A, catalytic domain / Beta-lactamase enzyme family / Beta-lactamase, class-A / Beta-lactamase / DD-peptidase/beta-lactamase superfamily / Beta-lactamase/transpeptidase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.43 Å
AuthorsFurey, I. / Palzkill, T. / Sankaran, B. / Hu, L. / Prasad, B.V.V.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI32956 United States
CitationJournal: J.Biol.Chem. / Year: 2021
Title: Local interactions with the Glu166 base and the conformation of an active site loop play key roles in carbapenem hydrolysis by the KPC-2 beta-lactamase.
Authors: Furey, I.M. / Mehta, S.C. / Sankaran, B. / Hu, L. / Prasad, B.V.V. / Palzkill, T.
History
DepositionFeb 1, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 26, 2021Provider: repository / Type: Initial release
Revision 1.1Jun 2, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jun 30, 2021Group: Structure summary / Category: audit_author
Revision 1.3Jul 21, 2021Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.title
Revision 1.4Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Beta-lactamase
B: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,1915
Polymers55,1222
Non-polymers693
Water9,332518
1
A: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,6073
Polymers27,5611
Non-polymers462
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,5842
Polymers27,5611
Non-polymers231
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)67.840, 71.660, 92.200
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Beta-lactamase


Mass: 27561.021 Da / Num. of mol.: 2 / Mutation: T215P
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae (bacteria)
Gene: KPC-2, bla, bla_1, bla_4, blaKPC, blaKPC-2, kpc2, B4U25_43300, BANRA_05566, C2U49_28140, C3F39_16210, C3F39_28515, C3F39_28975, C4Y50_021815, CK508_026140, DM059_13800, DM060_30440, DM078_ ...Gene: KPC-2, bla, bla_1, bla_4, blaKPC, blaKPC-2, kpc2, B4U25_43300, BANRA_05566, C2U49_28140, C3F39_16210, C3F39_28515, C3F39_28975, C4Y50_021815, CK508_026140, DM059_13800, DM060_30440, DM078_27040, DN589_26110, EAO17_31575, FKC87_27985, GF489_24625, GS419_28405, IPF_358, KP64477d_00006, KPC_069, p628KPC_020, pCRE79_15, pCT-KPC_129, pFOS18_014, pkp469IL_0095, pkp53il_00095, SAMEA3649709_04840, SAMEA3649772_05181, UC330_005, UC332_005, UC334_005
Production host: Escherichia coli (E. coli) / References: UniProt: Q93LQ9, beta-lactamase
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 518 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 1.98 Å3/Da / Density % sol: 37.77 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.15 / Details: 2.5M NaCl, 0.1M Sodium Acetate pH:5.15

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 0.999983 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 28, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.999983 Å / Relative weight: 1
ReflectionResolution: 1.43→46.1 Å / Num. obs: 82170 / % possible obs: 98.23 % / Redundancy: 1.9 % / Biso Wilson estimate: 14.68 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.02557 / Net I/σ(I): 11.12
Reflection shellResolution: 1.43→1.481 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.3081 / Mean I/σ(I) obs: 1.78 / Num. unique obs: 7735 / CC1/2: 0.832 / % possible all: 93.8

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
xia2data reduction
pointlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3C5A

3c5a


Resolution: 1.43→46.1 Å / SU ML: 0.1474 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.86 / Stereochemistry target values: CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1859 4155 5.06 %
Rwork0.1574 77985 -
obs0.1588 82140 98.24 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 20.25 Å2
Refinement stepCycle: LAST / Resolution: 1.43→46.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3884 0 3 518 4405
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053968
X-RAY DIFFRACTIONf_angle_d0.81815406
X-RAY DIFFRACTIONf_chiral_restr0.0746608
X-RAY DIFFRACTIONf_plane_restr0.0055710
X-RAY DIFFRACTIONf_dihedral_angle_d15.14781422
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.43-1.450.3311080.24252469X-RAY DIFFRACTION94.05
1.45-1.460.29161500.21922417X-RAY DIFFRACTION93.28
1.46-1.480.22721150.19692473X-RAY DIFFRACTION94.04
1.48-1.50.19431270.1752459X-RAY DIFFRACTION94.04
1.5-1.520.20291350.17082523X-RAY DIFFRACTION95.54
1.52-1.540.2221240.15952486X-RAY DIFFRACTION95.46
1.54-1.560.22331140.16032510X-RAY DIFFRACTION95.63
1.56-1.590.20121430.15712541X-RAY DIFFRACTION96.83
1.59-1.610.19711320.15342558X-RAY DIFFRACTION97.39
1.61-1.640.21561390.14732558X-RAY DIFFRACTION98.04
1.64-1.670.19881400.14392585X-RAY DIFFRACTION98.34
1.67-1.70.19051270.14682603X-RAY DIFFRACTION99.16
1.7-1.730.19121600.15772592X-RAY DIFFRACTION99.57
1.73-1.760.2331460.15412619X-RAY DIFFRACTION99.75
1.76-1.80.2131510.1512629X-RAY DIFFRACTION99.93
1.8-1.840.18741570.14472607X-RAY DIFFRACTION99.86
1.84-1.890.17531260.13992649X-RAY DIFFRACTION99.93
1.89-1.940.20391420.13632631X-RAY DIFFRACTION99.96
1.94-20.15971370.1362639X-RAY DIFFRACTION99.93
2-2.060.15731660.13572592X-RAY DIFFRACTION99.93
2.06-2.140.17221540.13532638X-RAY DIFFRACTION99.68
2.14-2.220.18071280.13742634X-RAY DIFFRACTION99.93
2.22-2.320.15841380.13912679X-RAY DIFFRACTION99.68
2.32-2.450.17811140.15052670X-RAY DIFFRACTION99.78
2.45-2.60.17521550.15652662X-RAY DIFFRACTION99.75
2.6-2.80.18681340.16482660X-RAY DIFFRACTION99.86
2.8-3.080.19261500.17762667X-RAY DIFFRACTION99.3
3.08-3.530.1641540.15872670X-RAY DIFFRACTION99.79
3.53-4.440.15641360.14852738X-RAY DIFFRACTION99.76
4.44-46.10.21421530.19032827X-RAY DIFFRACTION98.87

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